Have you tried using mri_warp_convert? You can convert from ITK format (ANTs) to M3Z via:
mri_warp_convert --initk antswarp.nii.gz --outm3z fswarp.m3z --insrcgeom src.nii.gz
This way you can also specify the missing source geometry information required for the m3z.
Andrew
________________________________________ From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, March 6, 2020 11:35 AM To: freesurfer@nmr.mgh.harvard.edu; Hoopes, Andrew Subject: Re: [Freesurfer] Converting ANTs nonlinear transform to .m3z
I think Andrew H might have a way to do this, but he's on vacation until next week. Try back then.
On 3/5/2020 12:29 PM, Ardesch, D.J. wrote:
External Email - Use Caution Dear FreeSurfer experts,
I am working on some monkey data and trying to get an accurate nonlinear transform to talairach space (talairach.m3z in the -careg stage). The problem is that the monkey brains look so different from the human brain that this registration ends up being very far off, even with an accurate talairach.lta.
As an alternative, I did a two-stage nonlinear registration using ANTs (first from subject to a macaque template and then from macaque template to talairach), which gives an accurate nonlinear transform. However, I can’t seem to convert this nonlinear transform file correctly from .nii.gz to the .m3z format that FreeSurfer needs to continue down the pipeline.
How would one go about converting the nonlinear transform from ANTs to a correct .m3z file?
Some other things I tried:
* I have tried a workaround in which I applied the inverse ANTs transform to the first frame of RB_all_2016-05-10.vc700.gca to get the talairach volume in subject space, and then ran mri_ca_register on that volume to obtain a talairach.m3z. That transform works but is still not accurate enough unfortunately.
* The nonlinear transform itself seems correct because when I apply it to the movable volume using ANTs the results are similar to:
mri_convert movable.mgz –apply_transform talairach.m3z -oc 0 0 0 movable_in_talairach.mgz where movable.mgz is the talairach volume in subject space and talairach.m3z is the transform made by mri_ca_register. The dimensions, orientation, and voxel size of movable_in_talairach.mgz and my own transformed volume are identical.
Any help would be greatly appreciated!
Platform: MacOS Mojave Version: FreeSurfer 6.0.0
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